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Sample GSM397523 Query DataSets for GSM397523
Status Public on Mar 31, 2010
Title InguinalFat.HFD.4
Sample type RNA
 
Source name Inguinal Fat: HFD
Organism Mus musculus
Characteristics strain: DBA/2J
tissue: Inguinal Fat
treatment: high fat diet
Extracted molecule total RNA
Extraction protocol Total RNA was isolated by TRIzolTM Plus after tissue homogenization (Invitrogen, Carlsbad, CA) according to the manufacturer’s protocols. RNA quality was assessed using an Agilent 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Palo Alto, CA). Total RNA was then reverse transcribed followed by second strand cDNA synthesis. An in vitro transcription (IVT) reaction was carried out incorporating biotinylated nucleotides according to the manufacturer’s protocol for Illumina® Totalprep RNA amplification kit (Ambion, Austin TX). 1.5µg biotin-labeled cRNA was hybridized onto Mouse-6 Expression BeadChips (Illumina, San Diego CA) for 16 hours at 55°C.
Label biotin
Label protocol Standard Illumina hybridization protocol
 
Hybridization protocol Standard Illumina scanning protocol
Scan protocol Probe set data, mean pixel intensities by bead type, were created using BeadStudio v3.1 and processed within the R/beadarray package
Description HFD: biological replicate 4
Data processing log2 transformation quantile normalization
 
Submission date Apr 24, 2009
Last update date Jan 21, 2010
Contact name Rachael S Hageman
E-mail(s) rachael.hageman@jax.org
Phone 216-906-2306
URL http://rachael.hageman@jax.org
Organization name The Jackson Laboratory
Street address 600 Main Street
City Bar Harbor
State/province ME
ZIP/Postal code 04609
Country USA
 
Platform ID GPL6105
Series (1)
GSE15822 High-fat diet leads to tissue-specific changes reflecting risk factors for diseases in DBA/2J mice

Data table header descriptions
ID_REF
VALUE log2 transformation and quantile normalization

Data table
ID_REF VALUE
ILMN_1243094 7.158910981
ILMN_1240307 7.2200622
ILMN_2486639 7.483721008
ILMN_1229397 7.794122375
ILMN_1225873 8.68833461
ILMN_1231752 7.215735944
ILMN_1257702 12.24220254
ILMN_1251148 7.084406063
ILMN_2691286 7.338173887
ILMN_1213242 7.109520239
ILMN_2728484 7.212096011
ILMN_2748584 10.28054055
ILMN_2519069 7.601329037
ILMN_1213815 6.931310759
ILMN_1237075 13.32393094
ILMN_2649966 15.04192454
ILMN_2699167 11.98528068
ILMN_2586958 8.023964122
ILMN_2760075 7.931326281
ILMN_1255729 7.56970733

Total number of rows: 46632

Table truncated, full table size 1133 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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